[med-svn] [soapsnp] 01/09: Move to standard conform directory layout
Andreas Tille
tille at debian.org
Thu Dec 28 07:17:47 UTC 2017
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tille pushed a commit to branch master
in repository soapsnp.
commit 814fc4ab97146b7214a9fd26896fc927352ea12e
Author: Andreas Tille <tille at debian.org>
Date: Fri Jun 8 10:08:01 2012 +0000
Move to standard conform directory layout
---
debian/README.Debian | 11 +++++++++++
debian/README.source | 5 +++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 34 ++++++++++++++++++++++++++++++++++
debian/copyright | 28 ++++++++++++++++++++++++++++
debian/docs | 1 +
debian/patches/Makefile.patch | 12 ++++++++++++
debian/patches/series | 1 +
debian/rules | 13 +++++++++++++
debian/source/format | 1 +
debian/upstream | 14 ++++++++++++++
debian/watch.ex | 23 +++++++++++++++++++++++
13 files changed, 149 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..23bf14a
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,11 @@
+soapsnp for Debian
+------------------
+
+** PACKAGING IS NOT YET COMPLETED **
+
+Ideas for improvements of this package:
+ * platform-specific optimisations
+ * debian/watch should be crafted
+ * we should have some public use cases together with getData
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 22 Apr 2012 01:26:41 +0200
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..6cbf68c
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,5 @@
+soapsnp for Debian
+------------------
+
+The man page was built with help2man and manually edited.
+
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..e15879d
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+soapsnp (1.03-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn)
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 22 Apr 2012 01:26:41 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..8dfb4ce
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,34 @@
+Source: soapsnp
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8.0.0), libboost-iostreams-dev
+Standards-Version: 3.9.3
+Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/soap/soapsnp/trunk
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/soap/soapsnp/trunk
+Homepage: http://soap.genomics.org.cn/soapsnp.html
+
+Package: soapsnp
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: genomics.cn-soapsnp
+Description: <insert up to 60 chars description>
+ For getting ideas on the cause of diseases or their response to
+ therapy, and for understanding either for a particular patient,
+ doctors around the globe are starting to look at the genes or the
+ whole genome and how that sequence is different from a healthy /
+ well responding individual.
+ .
+ SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis
+ Package). The program is a resequencing utility. It assembles the
+ consensus sequence for the genome of a newly sequenced individual based
+ on the alignment of the raw sequencing reads on a known reference. SNPs
+ can then be identified on the consensus sequence through the comparison
+ with the reference.
+ .
+ SOAPsnp uses a method based on Bayes' theorem (the reverse probability
+ model) to call consensus genotype by carefully considering the data
+ quality, alignment, and recurring experimental errors. All these kinds
+ of information was integrated into a single quality score for each base
+ in PHRED scale to measure the accuracy of consensus calling. Currently,
+ it supports the alignment format of SOAPaligner (soap2).
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..48e9955
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,28 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: soapsnp
+Source: <url://example.com>
+
+Files: *
+Copyright: 2008 BGI shenzhen <soap at genomics.org.cn>
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2012 Steffen Moeller <moeller at debian.org>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..8178c76
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+readme
diff --git a/debian/patches/Makefile.patch b/debian/patches/Makefile.patch
new file mode 100644
index 0000000..d89a5d0
--- /dev/null
+++ b/debian/patches/Makefile.patch
@@ -0,0 +1,12 @@
+Index: soapsnp-1.03/makefile
+===================================================================
+--- soapsnp-1.03.orig/makefile 2009-05-25 09:49:19.000000000 +0200
++++ soapsnp-1.03/makefile 2012-04-22 01:27:43.714978426 +0200
+@@ -1,6 +1,6 @@
+ DEFINE =
+ CXX = g++
+-CXXFLAGS = -fomit-frame-pointer -O3 -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0 #-MMD -MP -MF #-g3 -Wall -maccumulate-outgoing-args
++CXXFLAGS = -fomit-frame-pointer -O3 -ffast-math -funroll-loops #-mmmx -msse -msse2 -msse3 -fmessage-length=0 #-MMD -MP -MF #-g3 -Wall -maccumulate-outgoing-args
+
+ LFLAGS = -lz
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..5b1c0a4
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+Makefile.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..b760bee
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream b/debian/upstream
new file mode 100644
index 0000000..6651c34
--- /dev/null
+++ b/debian/upstream
@@ -0,0 +1,14 @@
+Contact: soap at genomics.org.cn
+Homepage: http://soap.genomics.org.cn/soapsnp.html
+Reference:
+ DOI: 10.1101/gr.088013.108
+ Eprint: http://genome.cshlp.org/content/19/6/1124.full.pdf+html
+ Journal: Genome Res.
+ PMID: 19420381
+ Author: Li R and Li Y and Fang X and Yang H and Wang J and Kristiansen K and Wang J.
+ Title: SNP detection for massively parallel whole-genome resequencing
+ URL: http://genome.cshlp.org/content/19/6/1124.long
+ Year: 2009
+ Volume: 19
+ Number: 6
+ Pages: 1124-1132
diff --git a/debian/watch.ex b/debian/watch.ex
new file mode 100644
index 0000000..bc2f478
--- /dev/null
+++ b/debian/watch.ex
@@ -0,0 +1,23 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 3 file
+version=3
+
+# Uncomment to examine a Webpage
+# <Webpage URL> <string match>
+#http://www.example.com/downloads.php soapsnp-(.*)\.tar\.gz
+
+# Uncomment to examine a Webserver directory
+#http://www.example.com/pub/soapsnp-(.*)\.tar\.gz
+
+# Uncommment to examine a FTP server
+#ftp://ftp.example.com/pub/soapsnp-(.*)\.tar\.gz debian uupdate
+
+# Uncomment to find new files on sourceforge, for devscripts >= 2.9
+# http://sf.net/soapsnp/soapsnp-(.*)\.tar\.gz
+
+# Uncomment to find new files on GooglePages
+# http://example.googlepages.com/foo.html soapsnp-(.*)\.tar\.gz
--
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